Last updated: 19:20, May 25, 2013
| Team | P | W | D | L | Pts | F | A | |
| 1 | Gillingham | 46 | 23 | 14 | 9 | 83 | 66 | 39 |
| 2 | Rotherham United | 46 | 24 | 7 | 15 | 79 | 74 | 59 |
| 3 | Port Vale | 46 | 21 | 15 | 10 | 78 | 87 | 52 |
| 4 | Burton Albion | 46 | 22 | 10 | 14 | 76 | 71 | 65 |
| 5 | Cheltenham Town | 46 | 20 | 15 | 11 | 75 | 58 | 51 |
| 6 | Northampton Town | 46 | 21 | 10 | 15 | 73 | 64 | 55 |
| 7 | Bradford City | 46 | 18 | 15 | 13 | 69 | 63 | 52 |
| 8 | Chesterfield | 46 | 18 | 13 | 15 | 67 | 60 | 45 |
| 9 | Oxford United | 46 | 19 | 8 | 19 | 65 | 60 | 61 |
| 10 | Exeter City | 46 | 18 | 10 | 18 | 64 | 63 | 62 |
| 11 | Rochdale | 46 | 16 | 13 | 17 | 61 | 68 | 70 |
| 12 | Southend United | 46 | 16 | 13 | 17 | 61 | 61 | 55 |
| 13 | Bristol Rovers | 46 | 16 | 12 | 18 | 60 | 60 | 69 |
| 14 | Wycombe Wanderers | 46 | 17 | 9 | 20 | 60 | 50 | 60 |
| 15 | Morecambe | 46 | 15 | 13 | 18 | 58 | 55 | 61 |
| 16 | York City | 46 | 12 | 19 | 15 | 55 | 50 | 60 |
| 17 | Accrington Stanley | 46 | 14 | 12 | 20 | 54 | 51 | 68 |
| 18 | Torquay United | 46 | 13 | 14 | 19 | 53 | 55 | 62 |
| 19 | Plymouth Argyle | 46 | 13 | 13 | 20 | 52 | 46 | 55 |
| 20 | Dagenham Redbridge | 46 | 13 | 12 | 21 | 51 | 55 | 62 |
| 21 | Barnet | 46 | 13 | 12 | 21 | 51 | 47 | 59 |
| 22 | Aldershot | 46 | 11 | 15 | 20 | 48 | 42 | 60 |


